Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor.

OBJECTIVE: Fusobacteria are not common nor relatively abundant in non-colorectal cancer (CRC) populations, however, we identified multiple Fusobacterium taxa nearly absent in western and rural populations to be comparatively more prevalent and relatively abundant in southern Chinese populations. We investigated whether these represented known or novel lineages in the Fusobacterium genus, and assessed their genomes for features implicated in development of cancer. METHODS: Prevalence and relative abundances of fusobacterial species were calculated from 3157 CRC and non-CRC gut metagenomes representing 16 populations from various biogeographies. Microbial genomes were assembled and compared with existing reference genomes to assess novel fusobacterial diversity. Phylogenetic distribution of virulence genes implicated in CRC was investigated. RESULTS: Irrespective of CRC disease status, southern Chinese populations harboured increased prevalence (maximum 39% vs 7%) and relative abundances (average 0.4% vs 0.04% of gut community) of multiple recognised and novel fusobacterial taxa phylogenetically distinct from Fusobacterium nucleatum. Genomes assembled from southern Chinese gut metagenomes increased existing fusobacterial diversity by 14.3%. Homologues of the FadA adhesin linked to CRC were consistently detected in several monophyletic lineages sister to and inclusive of F. varium and F. ulcerans, but not F. mortiferum. We also detected increased prevalence and relative abundances of F. varium in CRC compared with non-CRC cohorts, which together with distribution of FadA homologues supports a possible association with gut disease. CONCLUSION: The proportion of fusobacteria in guts of southern Chinese populations are higher compared with several western and rural populations in line with the notion of environment/biogeography driving human gut microbiome composition. Several non-nucleatum taxa possess FadA homologues and were enriched in CRC cohorts; whether this imposes a risk in developing CRC and other gut diseases deserves further investigation.

The human oral cavity microbiota composition during acute tonsillitis: a cross-sectional survey.

BACKGROUND: Microbial culture-based investigations of inflamed tonsil tissues have previously indicated enrichment of several microorganisms such as Streptococcus, Staphylococcus and Prevotella. These taxa were also largely reflected in DNA sequencing studies performed using tissue material. In comparison, less is known about the response of the overall oral cavity microbiota to acute tonsillitis despite their role in human health and evidence showing that their compositions are correlated with diseases such as oral cancers. In addition, the influence of subject-specific circumstances including consumption of prescription antibiotics and smoking habits on the microbiology of acute tonsillitis is unknown. METHODS: We collected oral rinse samples from 43 individuals admitted into hospital for acute tonsillitis and 165 non-disease volunteers recruited from the public, and compared their microbial community compositions using 16S rRNA gene sequencing. We assessed the impact of tonsillitis, whether subjects were prescribed antibiotics, the presence of oral abscesses and their smoking habits on community composition, and identified specific microbial taxa associated with tonsillitis and smoking. RESULTS: Oral rinse community composition was primarily associated with disease state (tonsillitis vs non-tonsillitis) although its effect was subtle, followed by smoking habit. Multiple Prevotella taxa were enriched in tonsillitis subjects compared to the non-tonsillitis cohort, whereas the non-tonsillitis cohort primarily showed associations with several Neisseria sequence variants. The presence of oral abscesses did not significantly influence community composition. Antibiotics were prescribed to a subset of individuals in the tonsillitis cohort but we did not observe differences in community composition associated with antibiotics consumption. In both tonsillitis and non-tonsillitis cohorts, smoking habit was associated with enrichment of several Fusobacterium variants. CONCLUSIONS: These findings show that the oral cavity microbial community is altered during acute tonsillitis, with a consistent enrichment of Prevotella during tonsillitis raising the possibility of targeted interventions. It also supports the possible link between smoking, Fusobacteria and oral cancers.

Effects of Echinocandins in Combination with Nikkomycin Z against Invasive Candida albicans Bloodstream Isolates and the fks Mutants.

We evaluated the in vitro and in vivo effects of nikkomycin Z combined with an echinocandin (anidulafungin or micafungin) against two Candida albicans isolates and their lab-derived echinocandin-resistant fks mutants with FKS1 S645Y and FKS1 S645P. Synergistic effects were observed in all tested strains (fractional inhibitory concentration index, <0.5). Enhanced survival was observed in an immunocompromised murine model (log-rank test, P < 0.02). Our study demonstrated the therapeutic potential of nikkomycin Z-echinocandin combinations in managing echinocandin resistance.

Ultrasound-guided synovial Tru-cut biopsy: indications, technique, and outcome in 111 cases.

OBJECTIVE: To investigate the diagnostic performance of ultrasound-guided synovial biopsy. METHODS: Clinical notes, pathology and microbiology reports, ultrasound and other imaging studies of 100 patients who underwent 111 ultrasound-guided synovial biopsies were reviewed. Biopsies were compared with the final clinical diagnosis established after synovectomy (n = 43) or clinical/imaging follow-up (n = 57) (mean 30 months). RESULTS: Other than a single vasovagal episode, no complication of synovial biopsy was encountered. One hundred and seven (96 %) of the 111 biopsies yielded synovium histologically. Pathology ± microbiology findings for these 107 conclusive biopsies comprised synovial tumour (n = 30, 28 %), synovial infection (n = 18, 17 %), synovial inflammation (n = 45, 42 %), including gouty arthritis (n = 3), and no abnormality (n = 14, 13 %). The accuracy, sensitivity, and specificity of synovial biopsy was 99 %, 97 %, and 100 % for synovial tumour; 100 %, 100 %, and 100 % for native joint infection; and 78 %, 45 %, and 100 % for prosthetic joint infection. False-negative synovial biopsy did not seem to be related to antibiotic therapy. CONCLUSION: Ultrasound-guided Tru-cut synovial biopsy is a safe and reliable technique with a high diagnostic yield for diagnosing synovial tumour and also, most likely, for joint infection. Regarding joint infection, synovial biopsy of native joints seems to have a higher diagnostic yield than that for infected prosthetic joints. KEY POINTS: • Ultrasound-guided Tru-cut synovial biopsy has high accuracy (99 %) for diagnosing synovial tumour. • It has good accuracy, sensitivity, and high specificity for diagnosis of joint infection. • Synovial biopsy of native joints works better than biopsy of prosthetic joints. • A negative synovial biopsy culture from a native joint largely excludes septic arthritis. • Ultrasound-guided Tru-cut synovial biopsy is a safe and well-tolerated procedure.

Blood microbial signatures associated with mortality in patients with sepsis: A pilot study.

Sepsis is a life-threatening illness caused by the dysregulated host response to infection. Nevertheless, our current knowledge of the microbial landscape in the blood of septic patients is still limited. Next-generation sequencing (NGS) is a sensitive method to quantitatively characterize microbiomes at various sites of the human body. In this study, we analyzed the blood microbial DNA of 22 adult patients with sepsis and 3 healthy subjects. The presence of non-human DNA was identified in both healthy and septic subjects. Septic patients had a markedly altered microbial DNA profile compared to healthy subjects over α- and ß-diversity. Unexpectedly, the patients could be further divided into two subgroups (C1 and C2) based on ß-diversity analysis. C1 patients showed much higher bacteria, viruses, fungi, and archaea abundance, and a higher level of α-diversity (Chao1, Observed and Shannon index) than both C2 patients and healthy subjects. The most striking difference was seen in the case of Streptomyces violaceusniger, Phenylobacterium sp. HYN0004, Caulobacter flavus, Streptomyces sp. 11-1-2, and Phenylobacterium zucineum, the abundance of which was the highest in the C1 group. Notably, C1 patients had a significantly poorer outcome than C2 patients. Moreover, by analyzing the patterns of microbe-microbe interactions in healthy and septic subjects, we revealed that C1 and C2 patients exhibited distinct co-occurrence and co-exclusion relationships. Together, our study uncovered two distinct microbial signatures in the blood of septic patients. Compositional and ecological analysis of blood microbial DNA may thus be useful in predicting mortality of septic patients.

Inhibitory effect of lactobacilli supernatants on biofilm and filamentation of Candida albicans, Candida tropicalis, and Candida parapsilosis.

Introduction: Probiotic Lactobacillus strains had been investigated for the potential to protect against infection caused by the major fungal pathogen of human, Candida albicans. Besides antifungal activity, lactobacilli demonstrated a promising inhibitory effect on biofilm formation and filamentation of C. albicans. On the other hand, two commonly isolated non-albicans Candida species, C. tropicalis and C. parapsilosis, have similar characteristics in filamentation and biofilm formation with C. albicans. However, there is scant information of the effect of lactobacilli on the two species. Methods: In this study, biofilm inhibitory effects of L. rhamnosus ATCC 53103, L. plantarum ATCC 8014, and L. acidophilus ATCC 4356 were tested on the reference strain C. albicans SC5314 and six bloodstream isolated clinical strains, two each of C. albicans, C. tropicalis, and C. parapsilosis. Results and Discussion: Cell-free culture supernatants (CFSs) of L. rhamnosus and L. plantarum significantly inhibited in vitro biofilm growth of C. albicans and C. tropicalis. L. acidophilus, conversely, had little effect on C. albicans and C. tropicalis but was more effective on inhibiting C. parapsilosis biofilms. Neutralized L. rhamnosus CFS at pH 7 retained the inhibitory effect, suggesting that exometabolites other than lactic acid produced by the Lactobacillus strain might be accounted for the effect. Furthermore, we evaluated the inhibitory effects of L. rhamnosus and L. plantarum CFSs on the filamentation of C. albicans and C. tropicalis strains. Significantly less Candida filaments were observed after co-incubating with CFSs under hyphae-inducing conditions. Expressions of six biofilm-related genes (ALS1, ALS3, BCR1, EFG1, TEC1, and UME6 in C. albicans and corresponding orthologs in C. tropicalis) in biofilms co-incubated with CFSs were analyzed using quantitative real-time PCR. When compared to untreated control, the expressions of ALS1, ALS3, EFG1, and TEC1 genes were downregulated in C. albicans biofilm. In C. tropicalis biofilms, ALS3 and UME6 were downregulated while TEC1 was upregulated. Taken together, the L. rhamnosus and L. plantarum strains demonstrated an inhibitory effect, which is likely mediated by the metabolites secreted into culture medium, on filamentation and biofilm formation of C. albicans and C. tropicalis. Our finding suggested an alternative to antifungals for controlling Candida biofilm.

Extent of Oral-Gut Transmission of Bacterial and Fungal Microbiota in Healthy Chinese Adults.

Recent studies have provided evidence on the presence of an oral-gut microbiota axis in gastrointestinal diseases; however, whether a similar axis exists in healthy individuals is still in debate. Here, we characterized the bacterial and fungal microbiomes in paired oral rinse and stool samples collected from 470 healthy Chinese adults by sequencing the 16S rRNA V3-V4 and ITS1 regions, respectively. We hypothesized that there is limited oral-gut transmission of both the bacterial and fungal microbiota in healthy Chinese adults. Our results showed that the oral and gut microbiota in healthy individuals differed in taxonomic composition, alpha and beta diversity, metabolic potential, and network properties. Bayesian analysis showed that the vast majority of subjects had negligible or low bacterial and fungal oral-to-stool contribution. Detailed examination of the prevalent amplicon sequence variants (ASVs) also revealed limited cases of sharing between the oral and stool samples within the same individuals, except a few bacterial and fungal ASVs. Association analysis showed that sharing of the potentially transmissible fungal ASVs was associated with host factors, including an older age and a higher body mass index. Our findings indicate that oral-gut transmission of both bacterial and fungal microbiota in healthy adults is limited. Detection of a large amount of shared bacterial or fungal members between the oral and gut microbiome of an individual may indicate medical conditions that warrant detailed checkup. IMPORTANCE The oral-gut microbiota axis in health is a fundamentally important and clinically relevant topic; however, our current understanding of it remains biased and incomplete. By characterizing the bacterial and fungal microbiomes in paired oral rinse and stool samples from a large cohort of healthy Chinese adults, here we provided new evidence that oral-gut microbiota transmission is limited in non-Western population and across biological domains. Our study has established an important baseline of a healthy oral-gut microbiota axis, with which other disease conditions can be compared. Besides, our findings have practical implications that detection of a large amount of shared bacterial or fungal members between the oral cavity and gut within the same individual as an indicator of potential medical conditions.

Overcoming the rising incidence and evolving mechanisms of antibiotic resistance by novel drug delivery approaches - An overview.

Antimicrobial resistance is a normal evolutionary process for microorganisms. Antibiotics exerted accelerated selective pressure that hasten bacterial resistance through mutation, and acquisition external genes. These genes often carry multiple antibiotic resistant determinants allowing the recipient microbe an instant "super-bug" status. The extent of Antimicrobial Resistance (AMR) has reached a level of global crisis, existing antimicrobials are no long effective in treating infections caused by AMR pathogens. The great majority of clinically available antimicrobial agents are administered through oral and intra-venous routes. Overcoming antibacterial resistance by novel drug delivery approach offered new hopes, particularly in the treatment of AMR pathogens in sites less assessible through systemic circulation such as the lung and skin. In the current review, we will revisit the mechanism and incidence of important AMR pathogens. Finally, we will discuss novel drug delivery approaches including novel local antibiotic delivery systems, hybrid antibiotics, and nanoparticle-based antibiotic delivery systems.

In vitro compatibility study of cephalosporin with intraocular irrigating solutions and intracameral medications.

BACKGROUND: To study the compatibility of cephalosporins with intraocular irrigating solutions and intracameral medications commonly used in cataract surgery. DESIGN: The was an in vitro experiment conducted in the Research Laboratory of the Department of Microbiology, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong. SAMPLES: Three cephalosporins--cefazolin, cefuroxime and ceftazidime--were separately diluted and mixed with irrigating solutions and intracameral medications to form 192 samples and 12 control solutions. METHODS: The cephalosporins were dissolved in normal saline and further diluted to the concentration of 1 mg in 0.1 mL with normal saline, Ringer's solution, balanced salt solution and fortified balanced salt solutions. These were mixed with balanced salt solutions or fortified balanced salt solutions, with adrenaline, acetylcholine or carbachol and kept at 37°C for 2 h. The concentrations of free cephalosporins were measured with rapid high-performance liquid chromatography at baseline (0 h) and at 2 h. MAIN OUTCOME MEASURES: Free concentrations of cephalosporins at 2 h were compared with mean baseline (0 h) value. A difference of 3 standard deviations or more was considered statistically significant. RESULTS: At 2 h there was a significant drop in the cefuroxime concentration in preparations in which cefuroxime was diluted with normal saline (P < 0.01). In all preparations, the final concentrations of cephalosporins were higher than the minimal inhibitory concentrations (MIC(90)) for microbials commonly isolated from the external eye. CONCLUSION: Cefazolin, cefuroxime and ceftazidime were compatible with irrigating solutions and intracameral medications commonly used in cataract surgery.

Longitudinal Genomic Characterization of Carbapenemase-producing Enterobacteriaceae (CPE) Reveals Changing Pattern of CPE Isolated in Hong Kong Hospitals.

An active, territory-wide, CPE surveillance program implemented from 2011 showed increasing levels of carbapenemase-producing Enterobacteriaceae (CPE) isolates from patients in Hong Kong hospitals. The molecular epidemiology of 567 CPE from patients of three of seven public hospital clusters in Hong Kong are described. During a 7-year period, the incidence of CPE isolation increased from 0.05 to 9.6/100 000 patient-days. The carbapenemase genes identified were polyclonal, including blaKPC, blaNDM and blaIMP, which were mainly associated with hospitalization overseas in previous years. However, increasing CPE isolation from patients without hospitalization overseas occurred in 2015, with blaNDM (52.6%) predominant followed by blaIMP (30.0%). Escherichia coli (46.4%) and Klebsiella spp. (38.3%) were the dominant species. Whole-genome sequencing was performed on 169 representative isolates with a combination of short and long reads using Illumina and Nanopore technology. Two distinct lineages of blaKPC-2-positive Klebsiella pneumoniae (ST11 and ST258) were identified with ST11 carrying yersiniabactin gene ybt-9 on ICEKp3. ST131 E. coli producing IMP-4 was present throughout the study period. The blaNDM and blaIMP genes were mainly carried in IncX3 and IncN-ST7 plasmids, respectively. blaOXA-48-like gene was carried in the IncX3 plasmid in E. coli and in the ColKP3 plasmid in K. pneumoniae. A lineage of K. pneumoniae with blaNDM-1 plus blaOXA-232 in distinct plasmids of IncF1B/IncHI1B was identified and associated with prior hospitalization overseas. This study highlights the threat of multiple types of CPE, with the predominance of blaNDM and blaIMP among CPE in our hospitals. Enhanced containment strategies are needed to mitigate the trend of rapidly rising CPE in healthcare settings.

Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease.

Fecal microbiota transplant (FMT) has emerged as a potential treatment for severe colitis associated with graft-versus-host disease (GvHD) following hematopoietic stem cell transplant. Bacterial engraftment from FMT donor to recipient has been reported, however the fate of fungi and viruses after FMT remains unclear. Here we report longitudinal dynamics of the gut bacteriome, mycobiome and virome in a teenager with GvHD after receiving four doses of FMT at weekly interval. After serial FMTs, the gut bacteriome, mycobiome and virome of the patient differ from compositions before FMT with variable temporal dynamics. Diversity of the gut bacterial community increases after each FMT. Gut fungal community initially shows expansion of several species followed by a decrease in diversity after multiple FMTs. In contrast, gut virome community varies substantially over time with a stable rise in diversity. The bacterium, Corynebacterium jeikeium, and Torque teno viruses, decrease after FMTs in parallel with an increase in the relative abundance of Caudovirales bacteriophages. Collectively, FMT may simultaneously impact on the various components of the gut microbiome with distinct effects.

Epidemiology and outcome of Candida bloodstream infection in an intensive care unit in Hong Kong.

OBJECTIVE: To study the epidemiology of Candida bloodstream infection in the Intensive Care Unit. DESIGN: Retrospective study. SETTING: A 22-bed, mixed medical and surgical Intensive Care Unit of a 1400-bed university teaching hospital in Hong Kong. PATIENTS: All adult patients (>18 years) who had at least one blood culture positive for Candida. RESULTS: During the 9 years of the study period, there were 128 patients with episodes of candidaemia (point prevalence, 9.6 per 1000 Intensive Care Unit admissions), 72 entailed albicans candidaemia and 56 non-albicans candidaemia. Albicans was still the predominant species, but the incidence of tropicalis was increasing. The median lengths of hospital and Intensive Care Unit stays prior to taking of the culture revealing candidaemia were 15 and 6 days, respectively. In all, 61% of patients did not have Candida colonisation within 2 weeks of their candidaemia. The main anti-fungal agents used were fluconazole and amphotericin B, but only 89 (70%) of the patients received appropriate anti-fungal treatment. Intensive Care Unit and hospital mortalities were 70% and 78%, respectively. Patients who did not receive appropriate treatment within 3 days had a worse outcome than those who did. CONCLUSIONS: Our data showed a high point prevalence of candidaemia in the Intensive Care Unit. Albicans was still the predominant species. Candidaemia occurred early during Intensive Care Unit stay, and a significant proportion of patients did not have prior fungal colonisation. Candidaemia in the Intensive Care Unit was associated with high morbidity and mortality. Many patients did not receive appropriately early anti-fungal therapy, and endured higher mortality than in the remainder.

Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles.

Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.

Genetic susceptibility to Tuberculosis: Interaction between HLA-DQA1 and age of onset.

Several genome-wide association studies (GWAS) identified new single nucleotide polymorphisms (SNPs) with susceptibility to Tuberculosis (TB). However, many of them were not replicated across ethnic groups. The cause of this phenomenon of genetic heterogeneity is uncertain. Here, we attempted to replicate and evaluate the mechanism that causes genetic heterogeneity in several putative TB predisposition loci found by previous GWAS, including chromosome 18q, ASAP1, DUSP14, and HLA-DQA1. A Chinese cohort of 1200 TB patients and 1280 population controls were genotyped. The results showed that genetic predisposition to TB might operate in an age-specific manner. While no significant association was found in the whole samples, a SNP of HLA-DQA1, rs9272785, showed suggestive association within the young-onset TB subgroup (onset at 20-40 years of age, N = 396). The results provide support for the hypothesis that there are different pathogenesis mechanisms causing clinical TB disease in different age groups, and that genetics probably play a substantial role only in young-onset TB.

Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling.

Proper preservation of stool samples to minimize microbial community shifts and inactivate infectious agents is important for self-collected specimens requiring shipment to laboratories when cold chain transport is not feasible. In this study, we evaluated the performance of six preservation solutions (Norgen, OMNI, RNAlater, CURNA, HEMA, and Shield) for these aspects. Following storage of human stool samples with these preservatives at room temperature for 7 days, three hypervariable regions of the bacterial 16S rRNA gene (V1-V2, V3-V4, and V4) were amplicon sequenced. We found that samples collected in two preservatives, Norgen and OMNI, showed the least shift in community composition relative to -80°C standards compared with other storage conditions, and both efficiently inhibited the growth of aerobic and anaerobic bacteria. RNAlater did not prevent bacterial activity and exhibited relatively larger community shift. Although the effect of preservation solution was small compared to intersubject variation, notable changes in microbiota composition were observed, which could create biases in downstream data analysis. When community profiles inferred from different 16S rRNA gene hypervariable regions were compared, we found differential sensitivity of primer sets in identifying overall microbial community and certain bacterial taxa. For example, reads generated by the V4 primer pair showed a higher alpha diversity of the gut microbial community. The degenerate 27f-YM primer failed to detect the majority of Bifidobacteriales. Our data indicate that choice of preservation solution and 16S rRNA gene primer pair are critical determinants affecting gut microbiota profiling. IMPORTANCE Large-scale human microbiota studies require specimens collected from multiple sites and/or time points to maximize detection of the small effects in microbe-host interactions. However, batch biases caused by experimental protocols, such as sample collection, massively parallel sequencing, and bioinformatics analyses, remain critical and should be minimized. This work evaluated the effects of preservation solutions and bacterial 16S rRNA gene primer pairs in revealing human gut microbiota composition. Since notable changes in detecting bacterial composition and abundance were observed among choice of preservatives and primer pairs, a consistent methodology is essential in minimizing their effects to facilitate comparisons between data sets.

Effectiveness of antimicrobial hospital curtains on reducing bacterial contamination-A multicenter study.

OBJECTIVE: To determine the efficacy of 2 types of antimicrobial privacy curtains in clinical settings and the costs involved in replacing standard curtains with antimicrobial curtains. DESIGN: A prospective, open-labeled, multicenter study with a follow-up duration of 6 months. SETTING: This study included 12 rooms of patients with multidrug-resistant organisms (MDROs) (668 patient bed days) and 10 cubicles (8,839 patient bed days) in the medical, surgical, neurosurgical, orthopedics, and rehabilitation units of 10 hospitals. METHOD: Culture samples were collected from curtain surfaces twice a week for 2 weeks, followed by weekly intervals. RESULTS: With a median hanging time of 173 days, antimicrobial curtain B (quaternary ammonium chlorides [QAC] plus polyorganosiloxane) was highly effective in reducing the bioburden (colony-forming units/100 cm2, 1 vs 57; P < .001) compared with the standard curtain. The percentages of MDRO contamination were also significantly lower on antimicrobial curtain B than the standard curtain: methicillin-resistant Staphylococcus aureus, 0.5% vs 24% (P < .001); carbapenem-resistant Acinetobacter spp, 0.2% vs 22.1% (P < .001); multidrug-resistant Acinetobacter spp, 0% vs 13.2% (P < .001). Notably, the median time to first contamination by MDROs was 27.6 times longer for antimicrobial curtain B than for the standard curtain (138 days vs 5 days; P = .001). CONCLUSIONS: Antimicrobial curtain B (QAC plus polyorganosiloxane) but not antimicrobial curtain A (built-in silver) effectively reduced the microbial burden and MDRO contamination compared with the standard curtain, even after extended use in an active clinical setting. The antimicrobial curtain provided an opportunity to avert indirect costs related to curtain changing and laundering in addition to improving patient safety.

Characterizing Mobilized Virulence Factors and Multidrug Resistance Genes in Carbapenemase-Producing Klebsiella pneumoniae in a Sri Lankan Hospital.

Limited data is available on the epidemiology and characteristics of carbapenem-resistant Enterobacteriaceae (CRE) and their associated plasmids or virulence determinants from Sri Lanka. Through whole genome sequencing of CREs from the intensive care units of a Sri Lankan teaching hospital, we identified a carbapenemase gene, blaOXA-181 in 10 carbapenemase-producing Klebsiella pneumoniae isolates (two strains of ST437 and eight strains of ST147) from 379 respiratory specimens. blaOXA-181 was carried in three variants of ColE-type plasmids. K. pneumoniae strains with ompK36 variants showed high minimum inhibitory concentrations to carbapenem. Furthermore, genes encoding for extended spectrum ß-lactamases (ESBL), plasmid-mediated quinolone resistance (PMQR) determinants (qnr, aac(6')-Ib-cr, and oqxAB) were present in all 10 strains. Amino acid substitution in chromosomal quinolone resistance-determining regions (QRDRs) gyrA (Ser83Ile) and parC (Ser80Ile) were also observed. All strains had yersiniabactin genes on mobile element ICEkp. Strict infection control practices and judicious use of antibiotics are warranted to prevent further spread of multidrug-resistant K. pneumoniae.

Diversity of macaque microbiota compared to the human counterparts.

Studies on the microbial communities in non-human primate hosts provide unique insights in both evolution and function of microbes related to human health and diseases. Using 16S rRNA gene amplicon profiling, we examined the oral, anal and vaginal microbiota in a group of non-captive rhesus macaques (N = 116) and compared the compositions with the healthy communities from Human Microbiome Project. The macaque microbiota was dominated by Bacteroidetes, Firmicutes and Proteobacteria; however, there were marked differences in phylotypes enriched across body sites indicative of strong niche specialization. Compared to human gut microbiota where Bacteroides predominately enriched, the surveyed macaque anal community exhibited increased abundance of Prevotella. In contrast to the conserved human vaginal microbiota extremely dominated by Lactobacillus, the macaque vaginal microbial composition was highly diverse while lactobacilli were rare. A constant decrease of the vaginal microbiota diversity was observed among macaque samples from juvenile, adult without tubectomy, and adult with tubectomy, with the most notable distinction being the enrichment of Halomonas in juvenile and Saccharofermentans in contracepted adults. Both macaque and human oral microbiota were colonized with three most common oral bacterial genera: Streptococcus, Haemophilus and Veillonella, and shared relatively conserved communities to each other. A number of bacteria related to human pathogens were consistently detected in macaques. The findings delineate the range of structure and diversity of microbial communities in a wild macaque population, and enable the application of macaque as an animal model for future characterization of microbes in transmission, genomics and function.

Characterizing 56 complete SARS-CoV S-gene sequences from Hong Kong.

BACKGROUND: The spike glycoprotein (S) gene of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) has been useful in analyzing the molecular epidemiology of the 2003 SARS outbreaks. OBJECTIVES: To characterize complete SARS-CoV S-gene sequences from Hong Kong. STUDY DESIGN: Fifty-six SARS-CoV S-gene sequences, obtained from patients who presented with SARS to the Prince of Wales Hospital during March-May 2003, were analysed using a maximum likelihood (ML) approach, together with 138 other (both human and animal) S-gene sequences downloaded from GenBank. RESULTS: The maximum-likelihood (ML) trees showed little evolution occurring within these 56 sequences. Analysis with the other sequences, showed three distinct SARS clusters, closely correlated to previously defined early, middle and late phases of the 2003 international SARS outbreaks. In addition, two new single nucleotide variations (SNVs), T21615A and T21901A, were discovered, not previously reported elsewhere. CONCLUSIONS: The ML approach to the reconstruction of tree phylogenies is known to be superior to the more popular, less computationally and time-demanding neighbour-joining (NJ) approach. The ML analysis in this study confirms the previously reported SARS epidemiology analysed mostly using the NJ approach. The two new SNVs reported here are most likely due to the tissue-culture passaging of the clinical samples.

Streptococcus suis in Hong Kong.

Streptococcus suis was isolated from 6.1% of raw pork meat from 3 of the 6 wet markets in 6 districts in Hong Kong. S. suis was particularly isolated in sites from the tongue, tonsil, bone, and tail, but not from lean meat/minced pork or internal organs. Isolates were confirmed by polymerase chain reaction using S. suis-specific primers, did not belong to serotype 2 using serotype 2-specific antiserum, and were clustered closely with other known serotypes by phylogenetic analysis. Ten strains from patients admitted to Hong Kong hospitals with sepsis or meningitis in the past 10 years all belonged to type 2, with closely related pulsed-field gel electrophoresis types that were distinct from the S. suis strains isolated from pork in this study. These methods may serve as useful tools in studying and enhancing our understanding of these infections in Hong Kong.